In direct seeding of non-coated rice seeds with a puddling seeder, seeds need to be stored to avoid overlapping of the timing of seed pretreatment with that of field preparation work. Assuming that seeds may be stored at room temperature for short-term storage but require lower temperatures for long-term storage, the optimum temperature for low temperature storage was investigated for both pre-germinated and root-elongated seeds. Seeds were incubated at 5°C, 10°C, and 15°C for 0, 5, 10, 14, and 21 days, before seeded in a growth cabinet to assess seedling emergence and growth. Compared to 5°C and 15°C, emergence and growth rates were not lowered in seeds stored at 10°C for more than 14 days. Therefore, 10°C was considered suitable for long-term storage. Then, both pre-germinated and root-elongated seeds were stored at room temperature (15.9°C–22.4°C) for 0 (control), 5, 10, and 15 days, and at 10°C for 20 to 29 days. When compared to the control, no significant differences were found in initial growth, establishment, and heading date of seeds stored at room temperature for 5 to 15 days and seeds stored at 10°C for 20 days. These results suggest that both pre-germinated and root-elongated seeds can be stored for up to 15 days at room temperature and up to 20 days at 10°C.